Articles
Page 27 of 30
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Citation: Journal of Cheminformatics 2011 3(Suppl 1):P42
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Homology modelling of metabotropic glutamate receptor 2
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P40 -
Docking and virtual screening of novel inhibitors for mono-ADP-ribosylating toxins
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P38 -
Predicting protein-protein interactions with DrugScorePPI: fully-flexible docking, scoring, and in silicoalanine-scanning
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P36 -
Application of biasing-potential replica exchange simulations for loop modeling and refinement of proteins in explicit solvent
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P33 -
Cavka – a new automatic pharmacophore elucidation method in progress
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P31 -
HYDEing the false positives – scoring for lead optimization
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P29 -
Use of large multiconformational databases with structure-based pharmacophore models for fast screening of commercial compound collections
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P27 -
Atomistic details of the phosphodiester cleavage of ribonuclease H
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P25 -
Virtual screening using structure-based consensus pharmacophore models and ensemble docking based on MD-generated conformations
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O23 -
Quantum chemical calculations on a unified pH scale for all phases
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P23 -
Towards targeting protein-protein interfaces with small molecules
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O21 -
LigpKa – a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P21 -
Predicting drug polypharmacology using a novel surface property similarity-based approach
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O19 -
Towards automated metabolome assembly: application of text mining to correlate small molecules, targets and tissues
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P19 -
Molecular simulation grid
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O17 -
Virtual screening workflow for glycogen synthase kinase 3β inhibitors: convergence of ligand-based and structure-based approaches
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P17 -
Thermodynamic models and factual data banks - ideal tools for the development of chemical processes
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O15 -
A framework and workflow system for virtual screening and molecular docking
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P15 -
Composite multiscale chemical informatics for formulations: challenges and solutions
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O13 -
Hydrogen placement in protein-ligand complexes under consideration of tautomerism
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P13 -
Constraint counting on RNA and ribosomal structures: linking flexibility and function
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O11 -
Searching substructures in fragment spaces
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P11 -
WizePairZ: a novel algorithm to identify, encode, and exploit matched molecular pairs with unspecified cores in medicinal chemistry
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O9 -
Visualization and virtual screening in molecular property spaces
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P8 -
Representation of Markush structures: from molecules toward patents
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O7 -
Free-Wilson in the 21st Century – evolution of a versatile toolkit for SAR analysis
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P6 -
Cheminformatics and computational chemistry in lead optimisation
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O5 -
Ketcher: web-based chemical structure editor
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P3 -
Making sure there's a "give" associated with the "take": producing and using open-source software in big pharma
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O3 -
German Conference on Chemoinformatics 2010 – organizers' notes
Citation: Journal of Cheminformatics 2011 3(Suppl 1):I1 -
Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P1 -
Hand in the snow
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O1 -
Interpreting linear support vector machine models with heat map molecule coloring
Model-based virtual screening plays an important role in the early drug discovery stage. The outcomes of high-throughput screenings are a valuable source for machine learning algorithms to infer such models. B...
Citation: Journal of Cheminformatics 2011 3:11 -
Review of "Data Analysis with Open Source Tools" by Philipp K Janert
Citation: Journal of Cheminformatics 2011 3:10 -
PubChem3D: Diversity of shape
The shape diversity of 16.4 million biologically relevant molecules from the PubChem Compound database and their 1.46 billion diverse conformers was explored as a function of molecular volume.
Citation: Journal of Cheminformatics 2011 3:9 -
Confab - Systematic generation of diverse low-energy conformers
Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-ene...
Citation: Journal of Cheminformatics 2011 3:8 -
Use of structure-activity landscape index curves and curve integrals to evaluate the performance of multiple machine learning prediction models
Standard approaches to address the performance of predictive models that used common statistical measurements for the entire data set provide an overview of the average performance of the models across the ent...
Citation: Journal of Cheminformatics 2011 3:7 -
FlaME: Flash Molecular Editor - a 2D structure input tool for the web
So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure edit...
Citation: Journal of Cheminformatics 2011 3:6 -
Modular Chemical Descriptor Language (MCDL): Stereochemical modules
In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure...
Citation: Journal of Cheminformatics 2011 3:5 -
PubChem3D: Conformer generation
PubChem, an open archive for the biological activities of small molecules, provides search and analysis tools to assist users in locating desired information. Many of these tools focus on the notion of chemica...
Citation: Journal of Cheminformatics 2011 3:4 -
jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints
The decomposition of a chemical graph is a convenient approach to encode information of the corresponding organic compound. While several commercial toolkits exist to encode molecules as so-called fingerprints...
Citation: Journal of Cheminformatics 2011 3:3 -
Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method
The reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex m...
Citation: Journal of Cheminformatics 2011 3:2 -
CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures
CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and ...
Citation: Journal of Cheminformatics 2011 3:1 -
Predicting cytotoxicity from heterogeneous data sources with Bayesian learning
We collected data from over 80 different cytotoxicity assays from Pfizer in-house work as well as from public sources and investigated the feasibility of using these datasets, which come from a variety of assa...
Citation: Journal of Cheminformatics 2010 2:11 -
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters
Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clu...
Citation: Journal of Cheminformatics 2010 2:10 -
Organization of GC/MS and LC/MS metabolomics data into chemical libraries
Metabolomics experiments involve generating and comparing small molecule (metabolite) profiles from complex mixture samples to identify those metabolites that are modulated in altered states (e.g., disease, dr...
Citation: Journal of Cheminformatics 2010 2:9 -
Basic primitives for molecular diagram sketching
A collection of primitive operations for molecular diagram sketching has been developed. These primitives compose a concise set of operations which can be used to construct publication-quality 2 D coordinates ...
Citation: Journal of Cheminformatics 2010 2:8 -
Collaborative development of predictive toxicology applications
OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical...
Citation: Journal of Cheminformatics 2010 2:7 -
WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications
In recent years, there has been a huge increase in the amount of publicly-available and proprietary information pertinent to drug discovery. However, there is a distinct lack of data mining tools available to ...
Citation: Journal of Cheminformatics 2010 2:6